So, going along with the secret alchemy, I just realized. Aether Foundation fits in perfectly with this. It's right in the name: aether. Aether is a supposed fifth element, associated with the well known elements: earth, water, fire, air. And aether is supposed to be the element where all the other elements came from.

So now I'm totally convinced that Aether Foundation created T:N and Gladion saved it. And it makes me wonder: do you think Aether Foundation have a bunch of other experiments lurking in some secret lab under their man-made island?